def test_convert_value_from_dg():
eps = 0.001
##############################################
# ORIGINAL = 'dg'
##############################################
dg = utils.unit_registry.Quantity(1, utils.unit_registry("kJ / mole"))
assert (pytest.approx(1.0, eps) == utils.convert_value(
dg, "dg", "dg", out_unit=utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
dg,
"dg",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.239, eps) == utils.convert_value(
dg,
"dg",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.6697, eps) == utils.convert_value(
dg, "dg", "ki").to(utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.6697, eps) == utils.convert_value(
dg, "dg", "ic50").to(utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.1741,
eps) == utils.convert_value(dg, "dg",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
assert "0.24 kcal/mol" == utils.convert_value(dg, "dg", "fakeObs")
def test_derive_observables():
for target in targets.target_dict.keys():
ligand_set = ligands.LigandSet(target)
for name, lig in ligand_set.items():
for i, t in enumerate(["dg", "ki", "ic50", "pic50"]):
lig.derive_observables(derived_type=t,
destination=f"DerivedMeasurement{i}")
for original_type in lig._observables:
if ("measurement", original_type) in list(lig._data.index):
assert lig._data[(f"DerivedMeasurement{i}",
t)] == utils.convert_value(
lig._data[("measurement",
original_type)],
original_type=original_type,
final_type=t,
)
# Test expected exception when trying to convert to unknown observable
with pytest.raises(
NotImplementedError,
match=f"Conversion to observable xxx not possible. "
f"Observable must be any of: dg, ki, ic50 or pic50.",
):
lig.derive_observables(derived_type="xxx",
destination=f"DerivedMeasurement")
# Test expected exception when trying to convert from unknown observable
for original_type in lig._observables:
if ("measurement", original_type) in list(lig._data.index):
lig._data.rename({original_type: "xxx"},
inplace=True,
level=1)
with pytest.raises(
ValueError,
match=f"No known measured observable found. "
f"Measured observable should be any of: dg, ki, ic50 or pic50.",
):
lig.derive_observables(
derived_type="pic50",
destination=f"DerivedMeasurement{i}")
def test_convert_value_from_ki():
eps = 0.001
##############################################
# ORIGINAL = 'ki'
##############################################
ki = utils.unit_registry.Quantity(1, utils.unit_registry.molar)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki, "ki", "dg", out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
ki, "ki", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
ki, "ki", "ic50").to(utils.unit_registry.molar).magnitude)
assert pytest.approx(0.0, eps) == utils.convert_value(ki, "ki",
"pic50").magnitude
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_value(ki, "ki", "fakeObs")
ki = utils.unit_registry.Quantity(1, utils.unit_registry("nanomolar"))
assert (pytest.approx(-51.69, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(-12.35,
eps) == utils.convert_value(ki, "ki", "dg").to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
ki, "ki", "dg",
temperature=300).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-47.04, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(ki, "ki", "ki").to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
ki, "ki", "ki", out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.0,
eps) == utils.convert_value(ki, "ki", "ic50").to(
utils.unit_registry("nanomolar")).magnitude)
assert pytest.approx(9, eps) == utils.convert_value(ki, "ki",
"pic50").magnitude
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_value(ki, "ki", "fakeObs")
def test_convert_value_from_ic50():
eps = 0.001
##############################################
# ORIGINAL = 'pic50'
##############################################
pic50 = utils.unit_registry.Quantity(0, "")
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300.0,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=273.0,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50, "pic50", "dg", out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
pic50, "pic50", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
pic50, "pic50", "ic50", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.0,
eps) == utils.convert_value(pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_value(pic50, "pic50", "fakeObs")
pic50 = utils.unit_registry.Quantity(9, "")
assert (pytest.approx(-51.69, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50, "pic50", "dg").to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50, "pic50", "dg",
temperature=300).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole"),
).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-47.04, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ki").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ic50").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ic50", out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(9,
eps) == utils.convert_value(pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_value(pic50, "pic50", "fakeObs")